The is very interesting.
bind-chroot has been a problem since 8.6 and needed to be removed because although it was OK to have it installed when Plesk was installed, when that package was ever updated it screwed up Plesk's configuration of named.
If I remember correctly, in one of the more recent updates Plesk has started to automatically remove it on install if it finds it on a system. This is a good thing as it prevents problems later on.
So I'm guessing something has changed, but what/when I don't know (worked fine for me in 6.3...so maybe it is 6.4 that's the problem?)
With bind-chroot removed, check to see what it says in /etc/sysconfig/named
It should be
ROOTDIR="/var/named/chroot"
OPTIONS="-c /etc/named.conf -u named -n 2"
Next, make sure that there's a symbolic link between /etc/named.conf and /var/named/chroot/etc/named.conf
e.g.
# ls -al /etc/named.conf
lrwxrwxrwx 1 root root 32 Jul 22 15:55 /etc/named.conf -> /var/named/chroot/etc/named.conf
Lastly, check the contents of /var/named/chroot/etc/named.conf
You should see data relating to sites on your server.
DO NOT make any changes to your system based on my post alone. Let's try and figure out what's happening before we go any further.